LAISHA Explains
Genetics and plant breeding

Transcription, translation and the genetic code

How a gene's DNA becomes RNA and then protein, the features of the genetic code, RNA processing in plants, and a worked transcription and translation.

Exam essential6 min readUpdated
On this page
  1. The central dogma
  2. Transcription
  3. The genetic code
  4. Translation
  5. Why it matters for agriculture
  6. Key points
  7. What the exams ask
  8. Questions people ask
  9. Sources
  10. Related on Laisha
  11. Discussion

A gene for disease resistance, drought tolerance or grain quality is just a stretch of DNA until the cell reads it. Reading happens in two steps: the DNA sequence is copied into a messenger molecule of RNA (transcription), and that message is decoded into a chain of amino acids, a protein (translation). The rules that link three-letter DNA "words" to amino acids form the genetic code.

Francis Crick summarised this flow of information in 1958 as the central dogma of molecular biology: DNA → RNA → protein. It is one of the most examined ideas in genetics and biotechnology, and the basis for genetic engineering in crops.

The central dogma

Information normally flows from DNA to RNA to protein. Exceptions refine rather than overturn it:

  • Reverse transcription: retroviruses and retrotransposons copy RNA back into DNA, discovered by H. Temin and D. Baltimore in 1970. Retrotransposons make up much of the genome of maize and wheat.
  • RNA replication: many plant viruses, such as tobacco mosaic virus, copy RNA directly into RNA.
  • Non-coding RNAs: many genes make RNAs that are never translated, such as ribosomal RNA, transfer RNA and the small RNAs that silence genes.

Information never flows back from protein to nucleic acid.

From gene to protein: the template strand of DNA is transcribed into messenger RNA with the same sequence as the coding strand except that U replaces T; the messenger RNA is read three bases at a time, each codon specifying an amino acid, so AUG GCU UGG AAA UAA gives methionine, alanine, tryptophan, lysine and then stop DNA coding5′ATGGCTTGGAAATAA3′ DNA template3′TACCGAACCTTTATT5′ transcription (RNA polymerase, in the nucleus) mRNA5′AUGGCUUGGAAAUAA3′ translation (ribosome, tRNA, in the cytoplasm) ProteinMetAlaTrpLysstop mRNA matches the coding strand, with U in place of T. Each three-base codon names one amino acid; AUG also means start, and UAA, UAG and UGA mean stop.
Transcription and translation of a short stretch of coding sequence. The mRNA matches the coding strand of DNA, with uracil in place of thymine, and is read three bases at a time.Diagram: Laisha, original.

Transcription

RNA polymerase reads the template (antisense) strand of DNA from 3′ to 5′, building RNA from 5′ to 3′. The RNA has the same sequence as the other, coding (sense) strand, except that U replaces T.

  1. Initiation: RNA polymerase, helped by transcription factors, binds a promoter upstream of the gene. Many eukaryotic promoters contain a TATA box about 25–30 bases upstream of the start; bacterial promoters have -10 and -35 sequences.
  2. Elongation: the polymerase unwinds a short stretch of DNA and adds ribonucleotides.
  3. Termination: transcription stops at a terminator sequence.

Bacteria have one RNA polymerase. Eukaryotes have three main ones: polymerase I (most ribosomal RNA), II (messenger RNA and many small RNAs) and III (transfer RNA and 5S RNA). Plants also have polymerases IV and V, which make RNAs that silence transposons and viruses.

Processing the message in eukaryotes

The first transcript, pre-mRNA, is modified before leaving the nucleus:

  • a 5′ cap (a modified guanine) is added, protecting the RNA and helping ribosomes bind;
  • a poly(A) tail of many adenines is added to the 3′ end;
  • introns, non-coding segments discovered by P. Sharp and R. Roberts in 1977, are removed by splicing, and the exons are joined. Alternative splicing lets one gene make several proteins.

In bacteria, transcription and translation happen together in the cytoplasm, with no splicing.

The genetic code

The code was cracked between 1961 and 1966. M. Nirenberg and J. H. Matthaei showed in 1961 that a synthetic RNA of only uracil (UUU…) produced a chain of phenylalanine; H. G. Khorana, Nirenberg and others then assigned all 64 codons.

Its features:

  • Triplet: each codon is three bases. Four bases give 43 = 64 codons.
  • Start and stop: AUG codes for methionine and also signals start; UAA, UAG and UGA are stop codons. So 61 codons specify 20 amino acids.
  • Degenerate (redundant): most amino acids have more than one codon; leucine, serine and arginine have six each, while methionine and tryptophan have one.
  • Wobble: the third base of a codon pairs loosely with the tRNA anticodon, so one tRNA can read several codons (Crick, 1966).
  • Non-overlapping and comma-less: codons are read one after another without gaps, so the reading frame matters.
  • Nearly universal: the same in bacteria, plants and animals, with small variations in mitochondria and some microbes. This is why a bacterial gene can be expressed in a plant.

Translation

Translation takes place on ribosomes, made of ribosomal RNA and proteins (80S in the cytoplasm of eukaryotes, 70S in bacteria, chloroplasts and mitochondria).

  • Transfer RNAs (tRNAs) carry amino acids. Each has an anticodon that pairs with a codon. Enzymes called aminoacyl-tRNA synthetases load each tRNA with the correct amino acid.
  • Initiation: the small ribosomal subunit binds the mRNA and finds the AUG start codon; the initiator tRNA carrying methionine pairs with it, and the large subunit joins.
  • Elongation: tRNAs enter the ribosome's A site, the growing chain is transferred to each new amino acid by a peptide bond (made by the ribosomal RNA itself), and the ribosome moves along one codon, shifting tRNAs to the P and E sites.
  • Termination: at a stop codon, release factors free the finished protein.

Several ribosomes can read one mRNA at once, forming a polysome.

Worked example

Transcribing and translating a gene fragment

The coding strand of a gene begins: 5′-ATG GCT TGG AAA TAA-3′.

  1. Template strand (complementary, antiparallel): 3′-TAC CGA ACC TTT ATT-5′.
  2. mRNA (same as coding strand, U for T): 5′-AUG GCU UGG AAA UAA-3′.
  3. Translation using the codon table: AUG = Met, GCU = Ala, UGG = Trp, AAA = Lys, UAA = stop.
  4. Protein: Met–Ala–Trp–Lys.
  5. tRNA anticodons (complementary to the codons, written 3′ to 5′): UAC, CGA, ACC, UUU.

A frameshift. If one base is inserted after AUG, for example a G, the message becomes AUG GGC UUG GAA AUA A…, which reads Met–Gly–Leu–Glu–Ile… instead: every codon after the insertion changes, which is why insertions and deletions usually destroy a protein's function.

Why it matters for agriculture

  • Transgenic crops need a plant promoter, such as the cauliflower mosaic virus 35S promoter, to switch on a foreign gene, and often a codon-optimised version of the gene; Bt cotton and maize carry rewritten bacterial cry genes that plants express well.
  • RNA interference uses double-stranded RNA to silence specific genes, the basis of some virus-resistant crops and RNA-based pesticides.
  • Gene editing changes specific bases in DNA, and the code predicts the effect on the protein.
  • Molecular markers and expression studies use transcription and translation to find genes for traits.

Key points

  • Central dogma: DNA → RNA (transcription) → protein (translation); exceptions include reverse transcription and RNA viruses.
  • RNA polymerase reads the template strand; mRNA matches the coding strand with U for T.
  • Eukaryotic pre-mRNA gets a 5′ cap, a poly(A) tail and splicing of introns.
  • The code is triplet, degenerate, non-overlapping, comma-less and nearly universal; 64 codons, 61 sense, 3 stop; AUG is start.
  • Ribosomes, tRNAs with anticodons and aminoacyl-tRNA synthetases translate mRNA in the A, P and E sites.

What the exams ask

  • School-leaving and entrance papers: the central dogma, the steps of transcription and translation, and features of the genetic code.
  • Degree and research-fellowship entrances: RNA polymerases, promoters, RNA processing, the Nirenberg–Matthaei experiment, wobble, ribosome sites, and translating sequences.
  • Biotechnology examinations: promoters and codon optimisation in transgenes, RNA interference, and gene regulation such as the lac operon.

Described in general terms: the kind of examination, not a past paper. Laisha never reproduces exam questions.

Questions people ask

Why is the code read in threes?

Two bases give only 16 combinations, too few for 20 amino acids; three give 64, enough for all, with spares that provide redundancy and stop signals.

Do all genes make proteins?

No. Some make functional RNAs, such as ribosomal and transfer RNAs, and many small RNAs that regulate other genes.

Why can a bacterial gene work in a plant?

The genetic code is nearly universal, so plant ribosomes read bacterial codons the same way. The gene still needs plant signals, a suitable promoter and terminator, and often codon changes to be expressed well.

Sources

  1. Crick, F. H. C. "On protein synthesis." Symposia of the Society for Experimental Biology 12, 138–163 (1958).
  2. Crick, F. "Central dogma of molecular biology." Nature 227, 561–563 (1970).
  3. Nirenberg, M. W. and Matthaei, J. H. "The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides." Proceedings of the National Academy of Sciences 47, 1588–1602 (1961).
  4. Alberts, B. et al. Molecular Biology of the Cell, 7th edition. W. W. Norton, 2022.
  5. Buchanan, B. B., Gruissem, W. and Jones, R. L. (eds) Biochemistry and Molecular Biology of Plants, 2nd edition. Wiley-Blackwell, 2015.

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